Marc Messerschmidt

Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures

The University at Buffalo theoretical databank of aspherical pseudoatoms has been tested in the refinement of high-resolution (HR; d(max) < or = 0.44 A) and truncated ;low-resolution (LR; d(max) = 0.83 A) X-ray diffraction data sets from the tripeptide Tyr-Gly-Gly monohydrate [Pichon-Pesme et al. (2000), Acta Cryst. B56, 728-737] and hexapeptide cyclo-(D,L-Pro)(2)-(L-Ala)4 monohydrate [Dittrich et al. (2002), Acta Cryst. B58, 721-727]. Application of the databank to LR data significantly lowers the conventional R factor, improves the determination of bonds and angles to within 0.002-0.003 A and 0.09-0.17 degrees of the values obtained from a complete multipolar refinement of HR data sets, improves the determination of phase angles by 2-6 degrees compared with the standard independent atom refinement (IAM), removes the majority of the bonding features from the residual Fourier difference maps and improves the atomic displacement parameters (ADPs) and the results of the Hirshfeld rigid-bond test. In the description of the aspherical density from experimental X-ray data, theoretical pseudoatoms were found to perform on the same level as the previously reported experimental databank [Pichon-Pesme et al. (1995), J. Phys. Chem. 99, 6242-6250; Jelsch et al. (1998), Acta Cryst. D54, 1306-1318], although no direct comparison of the two methods has been performed. The theoretical databank of aspherical pseudoatoms is shown to be a significant aid in the refinement of accurate experimental X-ray data from large molecular systems, in addition to its use in the reconstruction of molecular densities and the determination of electrostatic interaction energies.

Time-resolved synchrotron diffraction and theoretical studies of very short-lived photo-induced molecular species

Definitive experimental results on the geometry of fleeting species are at the time of writing still limited to monochromatic data collection, but methods for modifications of the polychromatic Laue data to increase their accuracy and their suitability for pump-probe experiments have been implemented and are reviewed. In the monochromatic experiments summarized, excited-state conversion percentages are small when neat crystals are used, but are higher when photoactive species are embedded in an inert framework in supramolecular crystals. With polychromatic techniques and increasing source brightness, smaller samples down to tenths of a micrometre or less can be used, increasing homogeneity of exposure and the fractional population of the excited species. Experiments described include a series of transition metal complexes and a fully organic example involving excimer formation. In the final section, experimental findings are compared with those from theoretical calculations on the isolated species. Qualitative agreement is generally obtained, but the theoretical results are strongly dependent on the details of the calculation, indicating the need for further systematic analysis.

The RATIO method for time-resolved Laue crystallography

A RATIO method for analysis of intensity changes in time-resolved pump-probe Laue diffraction experiments is described. The method eliminates the need for scaling the data with a wavelength curve representing the spectral distribution of the source and removes the effect of possible anisotropic absorption. It does not require relative scaling of series of frames and removes errors due to all but very short term fluctuations in the synchrotron beam.

Single-crystal-to-single-crystal E ! Z isomerization of tiglic acid in a supramolecular framework

The single-crystal-to-single-crystal E --> Z photoisomerization of tiglic acid (2,3-dimethylacrylic acid) occurs in the supramolecular crystals CECR-HTA x 2MeOH x 1.5H(2)O (1) (where HTA = tiglic acid, CECR = C-ethylcalix[4]resorcinarene) with the preservation of the crystal lattice, indicating the ;scaffolding effect of the molecular framework, which holds the crystal together notwithstanding the change in shape of the embedded guest molecules. A photostationary state is reached at a concentration of ca 30% of the Z isomers. A kinetic analysis shows the Z --> E back-reaction to proceed with a larger rate constant than the E --> Z isomerization.

Supramolecular solids and time-resolved diffraction

Supramolecular solids are an ideal medium for time-resolved diffraction studies at atomic resolution as they allow dilution of the active species, and the study of a species in different states of aggregation and different environments, but attention must be paid to excited-state quenching due to energy transfer. Crystallinity must be preserved up to reasonable product concentrations if chemical reactions are to be monitored at the atomic level.

Single-crystal-to-single-crystal e → Z and Z → e isomerizations of 3-chloroacrylic acid within the nanocavities of a supramolecular framework

Single-crystal-to-single-crystal E-->Z and Z-->E photo-isomerizations of 3-chloroacrylic acid (HClA) take place with full retention of the crystal lattice in the framework cavities of the supramolecular crystals CECR.HClA.2MeOH.1.5H(2)O (CECR = C-ethylcalix[4] resorcinarene); their progress has been monitored as the reaction proceeds.

Hydrogen-bond quenching of photodecarbonylation in the solid state and recovery of reactivity by co-crystallization

Intermolecular H-bonding between C=O (ketone) and HO (4-hydroxyphenyl) quenches photodecarbonylation of 2,2,4,4-tetramethyl-1,3-di(4-hydroxyphenyl)acetone 1 in the crystalline solid state, its reactivity is recovered by co-crystallization with the small organic molecule 4,4-bicyclohexanone.

Ligand-unsupported Au(I) chains with short Au(I)⋯Au(I) contacts

A new series of solids with ligand-unsupported Au(I) chains with short Au...Au contacts were synthesized; as Ag compounds with the same structure are known, the new phases now allow unbiased comparison of Ag...Ag and Au...Au metallophilic bonds not supported by bridging ligands, which shows the latter to be consistently shorter by 0.03-0.04 A.